*It will probably be infeasible to reconstitute the cyanobacteria oscillator in ''E. coli'', since we don't have any way to make phosphorylated KaiC do work, without cyanobacteria's myriad transcription factors

#***Has anyone read/heard Roderick MacKinnon, Nobel Prize winner for sussing out potassium ion channel structure? He gave these great talks a year or two back, and he showed a pretty animation of how the channels gate, using large motions of the six helices involved in the channel. They kind of twist out to open, twist in tight to close - like when you pull of a piece of those Twizzler's Pull and Peels, only in reverse, and all six at once. I know the scale of the ion channel is pretty low (I mean, it's meant to delive IONs, and dehydrated ones at that), but would it be possible to engineer something on a much larger scale w/ DNA helices?

+

****Has anyone read/heard Roderick MacKinnon, Nobel Prize winner for sussing out potassium ion channel structure? He gave these great talks a year or two back, and he showed a pretty animation of how the channels gate, using large motions of the six helices involved in the channel. They kind of twist out to open, twist in tight to close - like when you pull of a piece of those Twizzler's Pull and Peels, only in reverse, and all six at once. I know the scale of the ion channel is pretty low (I mean, it's meant to delive IONs, and dehydrated ones at that), but would it be possible to engineer something on a much larger scale w/ DNA helices?

-

*This idea of using origami for delivery only makes sense if:

-

#*The molecule we need to deliver can't be done more efficiently in some other way

-

#*The origami is big enough to hold a decent number of copies of the molecule

-

#*The big origami can get into the area it needs to be in in the first place

-

#Other Notes

+

*Sensibility

-

*In Chem 285, we spent a lot of time talking about problems with getting small molecules to get where they ought to get for efficacy. Maybe we could see if one of those molecules would make sense for delivery? (I didn't pay enough attention/don't have such a good long term memory to pull a molecule off the top of my head.)

+

**This idea of using origami for delivery only makes sense if:

+

***The molecule we need to deliver can't be done more efficiently in some other way

+

***The origami is big enough to hold a decent number of copies of the molecule

+

***The big origami can get into the area it needs to be in in the first place

+

*Let's do it!

-

*My pet interest is small non-coding RNA - ex. microRNAs, artificial RNAs used in RNAi - and another thing we saw in Chem 285 was the difficulty of getting RNA or even DNA into cells, to do their magic. What if we could make a structure that porated cells and inserted RNA or DNA+transcription-components? In other words, a virus, but low-damage - without the massive lysis we see for lots of viruses, maybe one hole per cell, or do it in such a way that the cell pinocytotes/phagocytotes the contents. And it has to be unhijackable by bad DNA.

+

*Other Notes

+

**In Chem 285, we spent a lot of time talking about problems with getting small molecules to get where they ought to get for efficacy. Maybe we could see if one of those molecules would make sense for delivery? (I didn't pay enough attention/don't have such a good long term memory to pull a molecule off the top of my head.)

+

**My pet interest is small non-coding RNA - ex. microRNAs, artificial RNAs used in RNAi - and another thing we saw in Chem 285 was the difficulty of getting RNA or even DNA into cells, to do their magic. What if we could make a structure that porated cells and inserted RNA or DNA+transcription-components? In other words, a virus, but low-damage - without the massive lysis we see for lots of viruses, maybe one hole per cell, or do it in such a way that the cell pinocytotes/phagocytotes the contents. And it has to be unhijackable by bad DNA.

+

**Last summer I was working on Yersinia enterocolitica, a relative of Yersinia pestis (ie. bubonic plague). The Yersinias and a few other types of bacteria use Type III secretion, which means they jab a hole into a host cell using their needle structure (which grows only when it gets close to the low-Mg2++ cell membrane environment) and import proteins (or, debatably, small non-coding RNAs) into the host. Could we use that? (Just an idea, I don't really know what it would be useful for, but it's kind of cool.)

+

**Does double-stranded DNA (dsDNA) get immunologically-chewed-up when it's free-floating around the body? That might be a problem. (I remember that bacterial single-stranded DNA did - or I think I remember that, along with CpG islands... man, I did really poorly in Immunology.)

-

*Last summer I was working on Yersinia enterocolitica, a relative of Yersinia pestis (ie. bubonic plague). The Yersinias and a few other types of bacteria use Type III secretion, which means they jab a hole into a host cell using their needle structure (which grows only when it gets close to the low-Mg2++ cell membrane environment) and import proteins (or, debatably, small non-coding RNAs) into the host. Could we use that? (Just an idea, I don't really know what it would be useful for, but it's kind of cool.)

-

-

*Does double-stranded DNA (dsDNA) get immunologically-chewed-up when it's free-floating around the body? That might be a problem. (I remember that bacterial single-stranded DNA did - or I think I remember that, along with CpG islands... man, I did really poorly in Immunology.)

Contents

6/19 (Monday)

Morning presentations

Cyanobacteria oscillator

It will probably be infeasible to reconstitute the cyanobacteria oscillator in E. coli, since we don't have any way to make phosphorylated KaiC do work, without cyanobacteria's myriad transcription factors

Has anyone read/heard Roderick MacKinnon, Nobel Prize winner for sussing out potassium ion channel structure? He gave these great talks a year or two back, and he showed a pretty animation of how the channels gate, using large motions of the six helices involved in the channel. They kind of twist out to open, twist in tight to close - like when you pull of a piece of those Twizzler's Pull and Peels, only in reverse, and all six at once. I know the scale of the ion channel is pretty low (I mean, it's meant to delive IONs, and dehydrated ones at that), but would it be possible to engineer something on a much larger scale w/ DNA helices?

Sensibility

This idea of using origami for delivery only makes sense if:

The molecule we need to deliver can't be done more efficiently in some other way

The origami is big enough to hold a decent number of copies of the molecule

The big origami can get into the area it needs to be in in the first place

Let's do it!

Other Notes

In Chem 285, we spent a lot of time talking about problems with getting small molecules to get where they ought to get for efficacy. Maybe we could see if one of those molecules would make sense for delivery? (I didn't pay enough attention/don't have such a good long term memory to pull a molecule off the top of my head.)

My pet interest is small non-coding RNA - ex. microRNAs, artificial RNAs used in RNAi - and another thing we saw in Chem 285 was the difficulty of getting RNA or even DNA into cells, to do their magic. What if we could make a structure that porated cells and inserted RNA or DNA+transcription-components? In other words, a virus, but low-damage - without the massive lysis we see for lots of viruses, maybe one hole per cell, or do it in such a way that the cell pinocytotes/phagocytotes the contents. And it has to be unhijackable by bad DNA.

Last summer I was working on Yersinia enterocolitica, a relative of Yersinia pestis (ie. bubonic plague). The Yersinias and a few other types of bacteria use Type III secretion, which means they jab a hole into a host cell using their needle structure (which grows only when it gets close to the low-Mg2++ cell membrane environment) and import proteins (or, debatably, small non-coding RNAs) into the host. Could we use that? (Just an idea, I don't really know what it would be useful for, but it's kind of cool.)

Does double-stranded DNA (dsDNA) get immunologically-chewed-up when it's free-floating around the body? That might be a problem. (I remember that bacterial single-stranded DNA did - or I think I remember that, along with CpG islands... man, I did really poorly in Immunology.)

Hope everyone's exams are going well, see you all soon!

from Tiff

(From the mailing list email I sent out awhile ago)

I'd just like to suggest that we consider doing something non-cloning based, as in Willliam Shih's DNA structure stuff.

Reasons Why:

cloning is probably going to be a LOT slower (and more difficult to get working, from personal experience) than what he was talking about

he's one of the world's experts, so I'm sure that with his guidance we could do something quick and error-free

it'll be so different and so much cooler than anything else any other group could think of, because it won't be bacterial-based

it's cutting edge

drug delivery systems are hot, and necessary, and this is seriously stuff NO ONE ELSE has ever thought of or done before

if we're going to try to make something with human (ie. medical) importance, starting in bacteria is good, but the eventual transition to eukaryotes is no fun to actually do (ie. transfection)

Reasons Against:

it won't be BBa_, so it might not be so legit in the competition

none of us probably have any experience doing stuff like that, but some of us already know how to clone (if I'm wrong, please correct me :))

from Dave

Hey everyone, here are some very high-level computer science-ish ideas I came up with tonight. I have no idea how hard these would be to implement, but I'll just throw these out there to get the spherical fullerene (haha) rolling:

I really liked the idea of containers built using scaffolded DNA origami, and exploring these might prove useful. Once we figure out how to seal the container and get it to open in response to certain stimuli, it might be interesting to create a set of these that respond to different stimuli. I assume that the lids would have to be different in each case, which might be hard to implement in some cases.

I was looking at MIT's 2004 brainstorming and saw some interesting stuff concerning insulin production/regulation in the bloodstream. We could even combine this with the containers, constructing cell "factories" that produce containers of insulin. These containers could then open when the concentration of blood glucose gets too high. I'm not exactly sure what benefits (if any) this extended scheme might provide, except maybe a quicker response to rising blood sugar levels since the insulin is already produced.

cell instant messaging: One cell can send a message that will propagate through the network and reach a unique destination cell. The important thing would be that the intermediate cells wouldn't interact with the message; they would simply know it was a message and pass it on. Sort of like passing the salt across the table without everyone using it on the way. Difficult? Possible? No idea. Although, it would be cool if a cell realized it had certain deficiencies and was able to "query" the cellular network to find a provider for what it needed. The part could then be passed back to the cell in need. Once again, the DNA containers could be used but I'm sure there are plenty of ways to do this. We would also need to figure out how to send queries across the network and send packages back, which could be difficult.

Once again, these are very high level ideas; it's pretty late and I haven't really researched anything in detail. I'm not sure what's feasible, but hopefully this leads to something useful. Feel free to comment/edit as you like.
~Dave

from Perry

Here are some ideas that were mentioned in the mcb100 group last fall,
when we were considering trying to develop our own system. some are
really bad/impractical, i know, but hopefully these start some
brainstorming.

- alarm clock, reporter in response to time lapse or sunlight

- stop watch, reporter expressed over time

- thermometer. different reporters or different amounts of one reporter
depending on temperature.

- chemical detector. one idea was ethanol, maybe detecting different
proofs; another idea was carbon monoxide.

- chip. 8 colonies = 8 bits? [i think this was mentioned in yesterday's
lecture as having been attempted with failure thusfar.]

- flashlight. bioluminescent reporter gene expressed in the absence of
light, or in other words, light acts as a repressor.

- litmus paper. one of two different colored reporter genes expressed
in acidic or basic pH.

- color-by-numbers. there are those books that have the outlines drawn
with numbers in the spaces, and a legend tells you which color you
should fill into which numbered spaces. so here we would have a lawn of
bacteria, separated physically into sections, and you would induce
different sections to show different colors according to the stimulus:
basically a multiple chemical detector system. the stimuli could
diffuse to activate all bacteria in a section, or the stimuli could
activate one bacterium which would send out the signal.

- wire. there was a BioWire project last year which send a coloration
signal down a line of bacteria. can an electric signal be carried,
maybe through ions? i guess this would require membrane ion-gates.